Chromosome-wide profiling of X-inactivation status and epigenetic regulation in opossum fetal brain and placenta

Experiment ID:SRP019501
Technology:RNA-Seq
Description:Evidence from a few genes of diverse species suggests that marsupial X-chromosome inactivation (XCI) is characterized by exclusive, but leaky, inactivation of the paternally derived X chromosome. To comprehensively study the mechanism of marsupial XCI, we profiled parent-of-origin-specific-allele expression, DNA methylation, and histone modifications in opossum fetal brain and extra-embryonic membranes. The majority (152/176) of X-linked genes exhibited paternally imprinted expression with nearly 100% maternal allele expression, whereas 24 loci (14%) escaped inactivation showing varying levels of biallelic expression. In addition to regulation by the non-coding RSX transcript, strong depletion of H3K27me3 at escaper gene loci indicates that histone states also influence opossum XCI. Notably, the opossum does not show an association between X-linked gene expression and promoter DNA methylation. Our study provides the first comprehensive catalogue of parent-of-origin expression status for X-linked genes in a marsupial and sheds light on the regulation and evolution of imprinted XCI in mammals. Overall design: Profiling of expression level and allele-specific expression ratios in embryonic day 13 opossum (Monodelphis domestica) fetal brain and extra-embyonic membranes by Illumina RNA-seq
Source:SRP019501  SRA
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Bulk RNA-Seq processed expression values in Monodelphis domestica

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Library ID
Identifier of the RNA-Seq library
Anat. entity ID
ID of the anatomical localization of the sample
Anat. entity name
Name of the anatomical localization of the sample
Anat. entity author annotation
Free text annotation of anatomical localization of the sample as provided by authors
Stage ID
ID of the developmental and life stage of the sample
Stage name
Name of the developmental and life stage of the sample
Stage author annotation
Free text annotation of the developmental and life stage of the sample as provided by authors
Sex
Annotation of the sex of the sample
Strain
Annotation of the strain of the sample
Time
Free text annotation of the time of sampling as provided by authors
Time unit
Unit for the time of sampling as provided by authors
Species
Physiological status
Physiological status of the organism at time of sampling
Technology
Sequencing platform
Sequenced transcript part
Possible values are: full length, all parts of the transcript are sequenced; 3': only the 3' end of the transcript is sequenced; 5': only the 5' end of the transcript is sequenced.
Fragmentation
Size of the RNA fragmentation
Run sequencing type
Paired-end or single-read run
Total read count
Total number of reads for the library.
Mapped read count
Number of reads that could be mapped to the transcriptome.
Total UMI count
Total number of individual RNA molecules (UMI) for the annotated sample. Only applicable for libraries producing UMIs.
Mapped UMI count
Number of UMIs that could be mapped to the transcriptome. Only applicable for libraries producing UMIs.
Distinct rank count
When performing a fractional ranking of the genes in the annotated sample, based on their expression level, number of distinct ranks observed, to have a value of the power for distinguishing expression levels. Used as a weight to compute a weighted mean rank accross samples for each gene and compute expression scores in Bgee.
Max rank
When performing a fractional ranking of the genes in the annotated sample, based on their expression level, maximum rank attained in the sample. Used to normalize ranks accross samples and compute expression scores in Bgee.
Link to processed expression values
See the processed expression value results for this assay
SRX250119UBERON:0005631 extraembryonic membraneextra-embryonic membranesUBERON:0000068 embryo stageembryonic day 13femaleLL2 mother (A0571) x LL1 father (A0578)NANAMonodelphis domesticaNAIlluminaIllumina HiSeq 2000FULL_LENGTH51single12298487178986063001986421960.5Browse results
SRX250120UBERON:0005631 extraembryonic membraneextra-embryonic membranesUBERON:0000068 embryo stageembryonic day 13femaleLL2 mother (A0571) x LL1 father (A0578)NANAMonodelphis domesticaNAIlluminaIllumina HiSeq 2000FULL_LENGTH51single10267622765344701001988621996.5Browse results
SRX250121UBERON:0005631 extraembryonic membraneextra-embryonic membranesUBERON:0000068 embryo stageembryonic day 13femaleLL1 mother (A0579) x LL2 father (A0573)NANAMonodelphis domesticaNAIlluminaIllumina HiSeq 2000FULL_LENGTH51single9712630564902266001970321884Browse results
SRX250122UBERON:0005631 extraembryonic membraneextra-embryonic membranesUBERON:0000068 embryo stageembryonic day 13femaleLL1 mother (A0579) x LL2 father (A0573)NANAMonodelphis domesticaNAIlluminaIllumina HiSeq 2000FULL_LENGTH51single9317651957611673001999322118Browse results
SRX250123UBERON:0000955 brainbrainUBERON:0000068 embryo stageembryonic day 13femaleLL2 mother (A0571) x LL1 father (A0578)NANAMonodelphis domesticaNAIlluminaIllumina HiSeq 2000FULL_LENGTH51single11144159572829528002130222958Browse results
SRX250124UBERON:0000955 brainbrainUBERON:0000068 embryo stageembryonic day 13femaleLL2 mother (A0571) x LL1 father (A0578)NANAMonodelphis domesticaNAIlluminaIllumina HiSeq 2000FULL_LENGTH51single10440173066208581002065622486.5Browse results
SRX250125UBERON:0000955 brainbrainUBERON:0000068 embryo stageembryonic day 13femaleLL1 mother (A0579) x LL2 father (A0573)NANAMonodelphis domesticaNAIlluminaIllumina HiSeq 2000FULL_LENGTH51single12327934280318552002129022938.5Browse results
SRX250126UBERON:0000955 brainbrainUBERON:0000068 embryo stageembryonic day 13femaleLL1 mother (A0579) x LL2 father (A0573)NANAMonodelphis domesticaNAIlluminaIllumina HiSeq 2000FULL_LENGTH51single10700185867872245002042422355.5Browse results
SRX250127UBERON:0005631 extraembryonic membraneextra-embryonic membranesUBERON:0000068 embryo stageembryonic day 13femaleLL1 mother (A0580) x LL1 father (A0578)NANAMonodelphis domesticaNAIlluminaIllumina HiSeq 2000FULL_LENGTH51single8917095054690266001983221957Browse results
SRX250128UBERON:0005631 extraembryonic membraneextra-embryonic membranesUBERON:0000068 embryo stageembryonic day 13maleLL1 mother (A0580) x LL1 father (A0578)NANAMonodelphis domesticaNAIlluminaIllumina HiSeq 2000FULL_LENGTH51single8090528549839574001956921802.5Browse results
SRX250129UBERON:0005631 extraembryonic membraneextra-embryonic membranesUBERON:0000068 embryo stageembryonic day 13femaleLL2 mother (A0572) x LL2 father (A0573)NANAMonodelphis domesticaNAIlluminaIllumina HiSeq 2000FULL_LENGTH51single5790683036108005001932821620Browse results
SRX250130UBERON:0005631 extraembryonic membraneextra-embryonic membranesUBERON:0000068 embryo stageembryonic day 13maleLL2 mother (A0572) x LL2 father (A0573)NANAMonodelphis domesticaNAIlluminaIllumina HiSeq 2000FULL_LENGTH51single7608244047498003001946321720Browse results
SRX250131UBERON:0000955 brainbrainUBERON:0000068 embryo stageembryonic day 13femaleLL1 mother (A0580) x LL1 father (A0578)NANAMonodelphis domesticaNAIlluminaIllumina HiSeq 2000FULL_LENGTH51single7834868348873360002008222117Browse results
SRX250132UBERON:0000955 brainbrainUBERON:0000068 embryo stageembryonic day 13maleLL1 mother (A0580) x LL1 father (A0578)NANAMonodelphis domesticaNAIlluminaIllumina HiSeq 2000FULL_LENGTH51single11104294669263977002054122384Browse results
SRX250133UBERON:0000955 brainbrainUBERON:0000068 embryo stageembryonic day 13femaleLL2 mother (A0572) x LL2 father (A0573)NANAMonodelphis domesticaNAIlluminaIllumina HiSeq 2000FULL_LENGTH51single7567246047313888002018622170Browse results
SRX250134UBERON:0000955 brainbrainUBERON:0000068 embryo stageembryonic day 13maleLL2 mother (A0572) x LL2 father (A0573)NANAMonodelphis domesticaNAIlluminaIllumina HiSeq 2000FULL_LENGTH51single7810792347550743002030622264.5Browse results

Showing 1 to 16 of 16 entries